Genes
as Technology? (Chapter 2: Error Detection)

This document expresses some thoughts
which have been rolling around my mind since 1980 when I rekindled by original
interest in biology. At that time, I was a computer technologist who
had recently decided that a career in software might offer more stability than
one in hardware. That same year I stumbled upon "The Eighth Day of
Creation" in a Toronto book store when something clicked in my head.
This webpage will be successful if I can light a similar spark in at least one
other person.

Simple Overview of
Error Detection in Computers

parity

originally known as vertical
parity check (VPC) because of the association with 9-track magnetic tape
technology

holding the tape horizontally, the parity-bit was at the top
of a vertical stack of 8-bits

you could paint a clear chemical (called magna-see)
on the tape. Once the chemical dried, you would apply "scotch tape" to
the magnetic tape. Then you would carefully remove the "scotch tape"
then apply it to a white piece of paper where the bits could be seen
with the naked eye.

8-data bits are written to
hardware (e.g. tape or memory) accompanied by a single parity bit
generated by the hardware adapter

odd parity:

if there are an even number of ones then hardware will also write a set (1) parity bit
so that the written character will contain an odd total of set bits

if there are an odd number
of ones then hardware will also write a clear (0) parity
bit so that the written character will contain an odd total of set
bits

even parity:

if there are an even number
of set data bits then hardware will also write a clear (0) parity
bit so that the written character will contain an even total of set
bits

if there are an odd number
of set data bits then hardware will also write a set (1) parity bit
so that the written character will contain an even total of set bits

when read back into the computer, the 8-data bits are
checked and then compared with the stored parity bit to determine
whether there has been any corruption (bit flips).

problems:

will only detect single bit
errors in a each 8-bit byte. Double bit errors pass through
unnoticed.

block check character (BCC)

originally known as longitudinal
parity check (LPC) because of the association with 9-track magnetic tape
technology

a block of characters (usually
256, 512 or 1024 bytes long) is followed by a machine generated character
which is an XOR (exclusive-OR) of the whole block

during a read operation, software
can attempt to repair data bits using both VPC + LRC as pointers into a
data matrix
(e.g.. parity errors in column 49 and row 3 point to a
single bit that could be repaired by software)

Simple Overview of Error Detection in Biology

Suffice it to say that enzymes exist
which step along DNA looking for incomplete base pairs (caused by ionizing
radiation, cosmic particles, environmental toxins, etc.) and can repair the
damage. However, if DNA damage occurs during cell division the damage is
usually copied (blind) which may cause one of the following events:

one daughter cell may die:
because the change was lethal

one daughter cell may mutate for
better:
because the change was accidentally beneficial

this is one basis for evolution
but the mutation needs to occur in the germ cell in order for the
mutation to be passed on to the gene pool. However, the germ cells have
the most amount of error detection/protection against DNA damage not to
mention that they're deep within the body.

one daughter cell may mutate for
worse:

because the change was not
beneficial but somehow the cell will now try to carry on in a different
way which may lead to

a genetic disease like
Huntington's Chorea

cancer

some types of dermoid tumors
contain teeth, hair, fingernails and even whole fingers. Since every
cell contains the whole genetic sequence for the whole body, either
these cells think they're somewhere else in the body (due to a break
down in inter-cellular communication) or they are just running amuck

most soma cells employ a
"telomere length" mechanism to control their speed of growth and
reduce the total number of times they may replicate (50 to 150 is
typical). The shorter the telomere the older the cell and the slower
it should grow. However, some tumors use the enzyme telomerase to
restore telomere length after cell replication. Provided there no
more fatal mutations and enough nutrients, these "anomalous life
forms" are effectively immortal until they kill their hosts.

because the change occurred in
an area of so-called junk DNA which has been abandoned long ago by
evolution

More to follow...

Recent Email Correspondence

(I've only published my side of the dialog)

Sent: 2003-08-27

First off, the ribosome "is" the CPU (but perhaps microprocessor
would be more accurate) as far as protein synthesis is concerned. As
far as I can tell, only certain portions of DNA are enabled at any one time
(when they are unwound) and then transcription enzymes read segments of the
enabled DNA copying them into messenger RNA (mRNA) segments. The ribosomes read
mRNA and then translate each triple base sequence into a single amino acid. At
this point, one must wonder what is going on here since amino acids are the
fundamental building blocks of proteins. Enzymes are simple proteins so they
"might" be mediating the whole program (possibly enabling a subroutine on some
other DNA sequence not yet unwound; possibly sending a signal to windup the DNA
sequence just transcribed; but who knows because this is just conjecture on my
part? It's just the way that I might have done it if I was designing the thing
from scratch). Everyone only thinks of muscle tissue when protein is mentioned
but it is the basis for everything from digestive enzymes, neurotransmitters,
some long chain hormones (not steroids but maybe longer chain stuff like insulin
etc.) so you can see how certain hormones might just express portions of DNA
which then might trigger some kind of reaction.

As I understand it, the biology community thinks of the whole genome as a set of
books (like encyclopedias). The chromosomes are the books and the genes are the
chapters. I don't know if genes are one single code sequence or a collection of
similar subroutines but I'd bet on the latter idea.

One interesting idea comes from something known as a
Dermoid tumor. When these
tumors are opened doctors sometimes find: whole teeth, hair, finger nails, whole
fingers, etc. Now we know that healthy cells are always communicating their
existence to there neighbors while tumor cells just do their own thing. Healthy
cells exchange messages like these "we are liver cells" which probably keeps the
"liver cell" program reinforced while all other programs are disabled.
In the case of Dermoid tumors, something must be happening that causes the wrong
program to become enabled and so a tooth starts growing where it shouldn't.

Sent: 2003-08-28

You mentioned the Human Genome Project and you are right about the
"bits" part. Most people don't know that a new informal project, called the Human
Proteome Project, will attempt to sequence all known proteins in terms of amino acids
(as well as their physical structure in three dimensions). Once you know which proteins have which sequence, you can go back to the
Human Genome
database to annotate it (e.g. this DNA sequence produces that protein
structure). This is very similar to what you would do when hacking a binary
program (like Windows) then working backwards to first produce assembly language
then annotate further until you have the original source code instructions (e.g.
C/C++)

You don't need to be a genius to recognize that biological sciences lurched
forward about the same time when computer systems dropped in price while
becoming much more powerful. The same thing happened in space sciences: apparently the
amount of information coming from the Hubble Space Telescope is an embarrassment
of new knowledge. Before Hubble, if you would have given a lecture on dark energy or dark matter
(aside from missing matter) you would have been laughed out of the
profession.

The "Folding@Home" project
(as well as other similar projects based upon BOINC) is a new twist on parallel computing individual PCs are doing molecular analysis for
new drugs and diseases.